Antifungal Therapy Eased IBD Activity, With Iliyan D. Iliev, PhD

Fluconazole treatment was associated with improved disease activity scores in patients with inflammatory bowel disease (IBD) and oral thrush, while a topical antifungal used to clear the same infection was not.

The finding comes from a 53-patient prospective observational study at Weill Cornell Medicine, published in Nature Medicine, that compared systemic fluconazole with a nystatin rinse in patients already being treated for mild oral thrush as part of routine IBD care.

Disease Activity Improved With Fluconazole in Both Ulcerative Colitis and Crohn's Disease

Disease activity was tracked using the partial Mayo score in patients with ulcerative colitis and the Harvey-Bradshaw Index in patients with Crohn's disease.

In an interview with HCPLive, Iliyan D. Iliev, PhD, professor of immunology in medicine and co-director of the microbiome core laboratory at the Jill Roberts Institute for Research in Inflammatory Bowel Disease at Weill Cornell Medicine, said both groups reported improved scores with fluconazole, alongside a decreased risk of disease progression over the 8-week follow-up period.

Iliev said the team could not obtain colonoscopy or biopsy data in such a short window, so clinical indices were the best available measure. He described the 53-patient cohort as an important first step rather than a conclusive result, noting that a placebo-controlled trial would be needed to confirm any clinical benefit.

A Placebo-Controlled Trial Is Needed Before Antifungal Cotherapy Becomes Standard of Care

"If you use them very long term, some of them can lead to liver toxicity and so on. They can lead to resistance," Iliev said of antifungal drugs, explaining why his team would not recommend extended use even if the approach is validated in a larger trial.

Iliev said the next step is a placebo-controlled study with longer follow-up and colonoscopy data, to determine whether the effect is durable and clinically meaningful. He described treatment aimed at the specific windows when Candida expands, rather than continuous antifungal use, as the more realistic model, with the goal of learning whether short antifungal courses could become standard of care for the subset of patients with IBD who experience fungal overgrowth.

"There is a very fine line. People call it dysbiosis; I would call it expansion of those populations. They find an environment where they will actually grow uncontrollably, and then the immune system reacts to that," Iliev said, describing the broader balance between commensal fungi and disease.

He added that fungal and bacterial species also play an important role in normal immune development, beyond their role in IBD.

Editor's Note: Iliev reported no relevant disclosures.

References

1. Pan X, Conroy A, Ngima TS, et al. Antifungal therapy improves microbiome dynamics in inflammatory bowel disease. Nat Med. Published online September 1, 2026. doi:10.1038/s41591-026-04616-y

2. Antifungal therapy shows potential for IBD patients with candida overgrowth. News release. Weill Cornell Medicine. EurekAlert! September 1, 2026. https://www.eurekalert.org/news-releases/1142314